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I made my changes using IDA but I don't know how to make the new file exe again

A: 

According to a discussion on OpenRCE, it seems that you cannot directly force IDA Pro to output an ".exe". What you can do is get it to produce a ".dif" and use that to patch the original ".exe".

To get IDA Pro to generate the ".dif": File->Produce file->Create

John Mulder